


The X-Files: The Next Generation season 1

by Bob79519



Series: How the X-Files should have ended post-season 8 [3]
Category: The X-Files
Genre: Fix-It, Mulder and Scully are retried because they deserve happiness damnit, as well as answers, how they should have done season 9, prepare for loads of questions to be revealed
Language: English
Status: In-Progress
Published: 2018-08-09
Updated: 2019-06-19
Packaged: 2019-06-24 08:12:41
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 19
Words: 10,566
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/15626502
Author URL: https://archiveofourown.org/users/Bob79519/pseuds/Bob79519
Summary: How season 9 should have gone, as well as alot of questions being given answers.





	1. End of The Beginning: prologue

There were only 4 people in the dimly-lit room. A brown-skinned man sat at the end of the table, a fat white-haired man at the the side, a red-haired woman sat on the other side and a brown-skinned woman sat the other end.

The white-haired man spoke first. "So are we going to discuss what to do, are we just going to discuss what we came here to discuss, or are we just going to sit here?" annoyance was evident in his tone.

The red-haired woman decided to start. "We're only dealing with something that could completely upset our plans, and make everything we've worked for all for nothing, again.

The brown-skinned woman sighed. "If that is the case, at least we'll be alive this time.

The brown-skinned man decided enough was enough. "While the aliens are busy dividing themselves about wherever or not they'll go ahead with the colonization of the Earth, we can at least start to get rid of the threats facing us!"

"The brown-skinned woman spoke. "And we can begin, by getting rid of a boy known as Gibson Praise."


	2. End of The Beginning: part 1

**Summary for the Chapter:**

> Doggett and Reyes begin working in the X-Files without Mulder and Scully

Special agent John Doggett entered the X-Files basement and looked around before sighing.

"This office is going to be very different without Mulder or Scully around." he mused out-loud.

His partner, Monica Reyes came up behind him. "Well I think they deserve to keep their happy ending, especially considering what they've been through over the past 8 years." she replied.

John nodded. It had been 6 months since William was born, and alot had happened since then. Mulder and Scully had got married, before moving away with William to an unremarkable house in Virginia. Scully had begun working in a hospital, while Mulder was staying home looking after William. Alvin Kersh had been arrested and sent to prison on charges of corruption and obstructing justice, and he was stated to be executed within the year.

Doggett sighed, he wanted to believe in the paranormal, he really did (especially when he was killed and came back to life). Unfortunately, the fact that his son's death was surrounded by the paranormal, meant that he would always have some skepticism towards it. Apparently, Kersh was part of the conspiracy that Mulder and Scully tried to expose for years before almost all of them were all killed.

Meanwhile, The Lone Gunmen's paper was selling better then ever and they gave that money to their intern: Jimmy Bond, to go and help him find Yves Adele Harlow, who was captured by a government agent known as Morris Fletcher. He had also captured the Lone Gunmen, but they were rescued by Jimmy and Kimmy the Geek.

"Anyway" Reyes said, pulling John out of his deep thoughts, "I think some change is required to better fit our personality's and life styles."

Doggett was curious what she had in mind. "Any ideas?"

"Getting myself a desk would be a good start. I don't understand why Scully never got one." Reyes mused.

"Apparently Mulder claimed it was because the basement was too small to have more than 1 desk." Dogget replied.

Reyes just laughed at this. "Well I can just set-up over there." She said, pointing to the almost never used dark corner of the basement. "Even if it means I won't be able to observe Mulder's fantastic pencil throwing skills" she said, looking up.

Doggett looked up as well and saw at least 100 pencils thrown into the ceiling above Mulder's desk.

But before he could ask about it, the phone rang. He answered it. "Hello?" he said. He then nodded a few times. "I understand, we'll be there as soon as possible." he said before hanging up.

"Who was that?" asked Reyes.

"That was Skinner." Doggett explained. "Since he's now deputy director, he won't have time to supervise us anymore. So, we're getting a new assistant director, and their waiting for us in his office."

"Let's go meet them." Reyes declared and they left the basement.

\-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

It turns out that the new assistant director, was someone that Doggett and Reyes had never heard of.

"Agent Doggett, Agent Reyes. I would like you to meet your new supervisor: Assistant director Anna Morales."

The new assistant director was wearing an ugly grey suit, with grey high-heel shoes, had white skin and brown hair.

"While I assure you that while my own interest in the X-Files remains strong, you'll be reporting directly to Morales from now on." Skinner explained.

Morales shook Doggett and Reyes's hands. "It's a surprise to meet you both." she said. "If I ever thought I would see the day that I became supervisor of the X-Files division, I would have thought I would be meeting the infamous Fox Mulder and Dana Scully."

Doggett cleared his throat. "Just over a year ago, I would have had the same thought."

"Me too." Mentioned Reyes.

"Well maybe it's for the better." Morales commented as she walked over the the desk and picked up a file. "I'm hoping to improve the reputation of the X-Files, and one of those ways, is by closing the open cases. she explained.

"What are your qualifications?" Doggett asked.

"A.D. Morales is the youngest member of the FBI to graduate at the top of her class and rise to this position." Skinner explained. "She's got some interesting ideas on how to focus and streamline the X-Files division."

Morales nodded. "While you've spent the last 6 months investigating and convicting ex-deputy director Kersh for his unforgivable crimes, a number of potential X-Files have surfaced. And their connected to the open cases."

"So what's our first case?" asked Doggett.

"Remember Gibson Praise?" asked Morales.

Doggett smiled. "How could I forget? he and Mulder are the reason why I ended up in the X-Files in the first place!"

"Well last night somebody broke into the house he was staying in New Mexico." Morales explained.

Doggett grew concerned. "Is he OK?"

Morales nodded. "He was able to hide until security barged in and killed his attacker. Afterwards, he asked for you."

"I'll head up there right now." Doggett replied.

"What about me?" Asked Reyes.

"Your going to autopsy the body and identify the man. More specifically, who he is and how he discovered Gibson's location." Morales ordered.

"Yes mam." Doggett replied and he and Reyes exited the room.

\-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

12 hours later...

Doggett stepped out of the airport and into the New Mexico heat.

"I forgot how hot it was." He commented while Reyes followed him into the rental car.

"Not as hot as actual Mexico. Maybe I'll tell you about it sometime." Reyes mentioned as Doggett dropper her off at the FBI field office located there.

Doggett was surprised. "You grew up in Mexico?"

Reyes shrugged. "Maybe I'll tell you about it sometime. Anyway good luck with Gibson." She said, getting out of the car and walking into the field office. Doggett just shook his head over how Quirky saw was and drove off to meet Gibson.

\-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Doggett entered the room Gibson was in.

"Hey Gibson, are you alright?" Doggett asked as he approached Gibson.

"I'm fine. Where Mulder?" Gibson replied.

Before Doggett could answer, Gibson started talking again. "Never mind, I'm happy Mulder and Scully got the happy ending they deserved, although I can sense you had a great time making sure that her brother did not ruin the wedding."

Doggett just smiled. "I can see why he and Mulder hate each other as much as they do. Anyway, do you know who broke in, and why?"

Gibson shook his head. "I'm afraid not, whomever these people are, they knew what they were doing. They knew about my ability to read people's minds and the man was wearing a helmet which blocked my ability to do so."

Doggett was still not convinced that Gibson could read minds. "So you don't know anything?"

Gibson shook his head. "As security shot him to death, they also shot his helmet off. In his last few seconds of life, I was able to read his mind and learnt that he was working for a company: the Strughold Mining Company."

Doggett frowned. "Strughold Mining Company, I think I've heard of that name before."

"I never have either." Gibson explained.

Doggett thought for a bit. "I remember reading about that in the X-Files. It was something Mulder wrote when he painstakingly used his spare time to re-write all of the X-Files that had been lost when their office was burned."

"The man also thought about an oil pipe-line in Wyoming." Gibson explained.

Before Doggett could ask about what he meant, his phone rang. "Doggett here."

"John, it's Monica. I've finished the autopsy of the man who broke in." Reyes announced.

"OK." Doggett replied, feeling uneasy.

"I ran the man's prints through every database imaginable, I found nothing. It's like somebody erased this man's existence. The only notable feature about this man, is that he has grey-hair." Reyes explained. "Anyway, how did things go with Gibson?"

Doggett then explained to Monica about his conversation with Gibson.

"I see." She said at last. "Give me a minute, I will see what I can find."

Reyes sat down and typed on the computer.

"OK, The Strughold Mining Company has an oil pipeline under construction in Wyoming. There's a protest by environmentalists trying to stop the construction."

"I think something bad is going to happen there." Doggett commented.

"I can't find out anything about who the CEO of the company is, or where there headquarters are." Reyes said, evidently annoyed.

"Gibson, is there anyone who could have information about the company?" Doggett asked Gibson.

"Marita Covarrubias." Gibson replied.

"Wasn't she one of Mulder's contacts?" Reyes asked.

"She is, I'll tell you where you can find her." Gibson said, and proceeded to do that.

"How do you know all this?" Doggett asked once Gibson had finished telling Monica where Marita Covarrubias was.

"She visited me shortly after you last saw me, and made sure I was alright." Gibson explained.

"You 2 know each other?" asked Doggett.

"Yes. But I don't time to explain." Gibson replied. "You have to get to Wyoming and figure out what is going on there, while your partner, Monica Reyes, goes to meet Marita. I'll contact her to let her know that Reyes is coming."

Doggett nodded. "Stay safe." He said, and left.

**Notes for the Chapter:**

> If your wondering if the man who tried to kidnap Gibson Praise sounds familiar, it's because it's the grey-haired man who used to work for CSM. Unfortunately, he abruptly vanished (unlike all the other Men in Black, who were all killed off). So I decided to fix that, so he's moved up in the ranks.


	3. End of The Beginning: part 2

**Summary for the Chapter:**

> Reyes gets a lot of answers from a certain blonde.

The next day...

Reyes arrived at the address Gibson had given her, she knocked on the door. A blonde woman wearing a business suit opened the door.

"You must be special agent Monica Reyes." said the woman. "I am Marita Covarrubias." She let Reyes inside.

"Gibson said your were coming." Marita explained. "He said that you might have some questions."

Reyes nodded. Marita indicated that they should sit down on the sofa, which they did.

"First question, how did you meet Gibson?" Reyes asked.

"It was shortly after the conspiracy known as the Syndicate were wiped out." Marita explained. "Gibson found me at the Disease Control facility at Fort Marlene. He and the alien with him, who nursed me back to health."

Reyes was surprised. "Why did the alien help you?"

"Because he was an undercover agent working for the alien rebels." Marita explained.

"Weren't they the ones who wiped the Syndicate?" Reyes asked.

"They did." Marita confirmed. "They made sure Gibson was out of anyone's hands. He helped me get my job back at the UN, while I sent him to New Mexico for his safety."

"OK." Reyes replied. "Who are the alien rebels and why are the rebels?"

"That's a long story." Marita said.

"Well I've got nothing else better to do." Reyes teased.

Marita sighed. "Alright." She cleared her throat. "The reason why the aliens, who are known as the colonists, wanted to colonize the Earth in the first place, was because the planets they had already colonized were starting to run out of resources. When they did a recon and discovered that they were billions of humans, they began to panic because there were only a few thousand of them."

Reyes then began to fill in the blanks herself. "That's when the discovered the Syndicate and made the deal with them to develop the human/alien hybrids?"

Marita nodded. "The colonists had calculated that they would run out of resources on December 22,2012. So they gave the Syndicate that deadline."

"So they lied to the Syndicate about how many of them there were?" Reyes asked.

"They did." Marita confirmed. "And being the fools they were, they fell for it. They then spent over 20 years developing the hybrids. However, quite a few of the colonists thought the plan was stupid and decided to stop it."

"You mean the alien rebels?" Reyes asked.

"Yes. At first they wanted to capture the only successful hybrid: Cassandra Spender. But when that failed, they decided to just kill her." Marita explained.

"And I presume with Cassandra's death, the colonists panicked?"

"You presume correctly. Since the aliens couldn't make their own hybrids due to lack of resources, they started to take some desperate measures to colonize the Earth." Marita explained.

Reyes remembered reading the X-Files. "The alien spaceship Scully found, which had inscriptions of various religious texts."

"Those were planted by the religious order of the colonists, known as the Acolytes."

Reyes frowned. "The X-Files never mentioned the Acolytes."

"That's because Mulder and Scully never encountered them." Marita explained. "There plan was to trick humanity into believing that the colonists had created them and were to be accepted as gods and take over the Earth."

"But that didn't work." Reyes clarified.

Marita nodded. "They decided to have one last try and developed the Super Soldiers. However, more and more colonists were defecting to the rebels, so they needed to come up with a false hope. When they found out Dana Scully was pregnant, they used that as an excuse to create the super solders. They killed anyone trying to interfere or study the baby and said that if it had powers, then they would colonize the Earth. If it didn't, they they would look elsewhere to colonize."

"But William is just a normal child, with no powers or anything." Reyes stated.

"The Colonists and the rebels stopped fighting and went off to look for other planets to colonize." Marita explained.

"OK, I understand." Reyes stated. "But what happened after you and Alex Alex Krycek after you 2 sent Mulder to Oregon?"

"Alex killed C.G.B Spender by pushing him down the stairs. He then burned the body afterwards, just to make sure he didn't escape certain death, again." Marita explained. "Afterwards, me and Alex discovered that C.G.B Spender had been busy getting ready to protect Mulder.

Reyes frowned. "What do you mean?"

"We discovered a briefcase with documents, passports, and receipts Spender's car. They revealed that he had been going to the doctor's for over a year while posing as Mulder."

"So that's everyone thought Mulder had a brain disease, I always thought that made no sense." Reyes mused.

Marita ignored her. "We discovered that since Spender knew that he was going to die within the month, especially with the ship in his possession he would have everything in place. When he died, he died as Mulder. He was giving Mulder the ultimate gift. Anonymity. For all intents and purposes, when Spender died, Mulder died. He would have no longer existed. Its was Spender's last way to ensure Mulder would be protected. He probably arranged for someone to contact Mulder upon his death. Mulder would have been given Spender's place as the head of the new syndicate he wanted to create. With a new life, a new name. And according to the bank statements, he would have inherited billions."

"But that never happened." Reyes exclaimed.

"Alex gave the information to the Alien bounty hunter, who in return, promised Alex a place with them, after they colonized the Earth." Marita explained.

"They also used the information to cast doubt on Mulder and Scully's relationship." Reyes realized. "I never accepted the fact Mulder was going all around the country in the weeks leading up to his abduction, he was too busy having sex with Scully."

They both laughed at that comment.

"So you and Alex parted ways after that?" Asked Reyes.

"That is correct." Marita continued. "He started to work for the aliens, and started doing their dirty work."

"So why did he protect Scully's baby before it was born?" Reyes asked in confusion.

"Because he wanted to give humanity 1 last chance." Marita explained. "When they didn't take that chance, he fully teamed up with the colonists and was killed for it."

"What about you?" Reyes asked.

"A few months after I last saw Alex, I was contacted by a new conspiracy, calling themselves the NeoSyndicate. They wanted me to join them in whatever plan they have to convince the aliens to colonize the Earth." Marita explained.

"And what did you say to that?" Reyes asked.

"I said no. I'm done with that life. Now, I just want to do me job as Special Representative to the Secretary-General of the United Nations, and not be involved with anymore conspiracy's." Marita finished.

"Fair enough." Reyes said, standing up. "Thanks for the information, it will be a big help." They shook hands and Reyes left.

**Notes for the Chapter:**

> Author's note: And I have successfully answered a bunch of questions and fixed the stupidity of Mulder's brain disease in season 8!


	4. End of The Beginning: part 3

**Summary for the Chapter:**

> Doggett investigates the oil pipeline.

Later that same day...

Doggett arrived at the oil pipeline in Wyoming. The ground was ugly brown, the pipeline blood red and there were loads of construction workers, FBI agents and protesters, who were only kept out by a barbed wire fence.

Doggett wasn't here for the protester's though, he was here to figure out why the man who broke into Gibson's home, was thinking about this oil pipeline. His first move was to find the foreman. After wandering about for a bit, he found someone who looked like he was in charge. While he was wearing everything the construction workers were wearing, his voice and attitude made it look like he was in charge.

"Let's get this walkthrough set up so we can finish once we came back from lunch, I don't want hungry workers constructing this line!" he was saying to his presumed second-in-command.

Sensing his opportunity, Doggett stepped forward. "Excuse me, I'm looking for the foreman."

"I'm the foreman, what's this about?" Asked the foreman.

So far, so good "Special agent John Doggett, FBI. We're investigating a potential threat to the oil pipeline, have you noticed anything out of the ordinary?" he asked.

"Not unless our 'occupied' cheering section took a bath this morning!"

The second-in-command laughed. "ha! Good one chief!"

"So maybe they should find a cleaner way to spend their day?" Doggett rhymed.

"Yeah!" said the foreman, like it was the most obvious thing in the world.

Seeing that this was getting him nowhere, Doggett decided to take the initiative. "I'll take a look around." He walked off, not noticing the glare the foreman was giving him.

About 5 minutes later, Doggett was walking by a door, when his I.D. tag flew off stuck to the door.

"Yeah, I'm going to need that back." He mused as he grabbed the I.D. tag and opened the door. He was surprised by what he saw. "Funny, I didn't know that crude oil glittered like jewelry."

"You know nothing, John Doggett." A familiar voice said behind him.

Doggett spun around, and saw that the foreman was behind him Only now, he was dressed in a black robe, something similar to Darth Sidious in the Star Wars prequels.

"And now, you will die for interfering with our plans for the last time!" He shouted and pulled his hand out of his pocket, revealing a knife. And charged at Doggett. Doggett pulled his gun out and was about to shout 'Freeze!', when there was a gunshot.

The foreman froze before looking down and seeing a huge hole in his chest, with blood pouring out faster than the lifts in the Shining. He then fell onto the floor, dead.

Doggett looked up at his savior, and saw a generic FBI agent, standing there with a smoking shotgun. "I saw the foreman change into these suspicious robes and get a knife, so I followed him, saw him try to kill you, so I killed him first." explained the agent.

Doggett nodded, while he was unhappy that the foreman was dead and could not be interrogated for any information, he was thankful to be alive. "What's your name?"

"Peyton Ritter" said the FBI agent, and he and Mulder shook hands.

\-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

48 hours later...

Doggett and Reyes sat in A.D. Morales's office in the FBI headquarters in Washington D.C.

"Thanks to your efforts agent Doggett, we were able to prevent a massive fraud scheme." Morales was saying. "We also discovered that somebody, presumably the foreman, had put magnetite into the pipeline. The Strughold Mining Company is being compensated millions of dollars." She said proudly. "You've already improved the reputation of the X-Files, well done." She said, smiling.

"Doesn't agent Ritter deserve any credit?" Doggett asked. 

"NO!" Morales almost shouted, before taking a deep breath. "Shortly before Mulder and Scully stopped working for Kersh and went back to the X-Files, he sent her with agent Ritter on a case. To make a long story short, agent Ritter 'accidentally' shot Scully and the suspect. The suspect died and Scully only miraculously survived." She said, anger evident in her voice. "He was supposed to be fired, but Kersh was able to pull a few strings and instead, he was transferred to another field office." She explained. "I made a deal with him, he gets to stay in the FBI, as long as he doesn't get credit or gets involved with the X-Files."

Doggett nodded. Morales seemed unusually emotional, but he just presumed that it had something to do with the fact that she was talking about with 1 of the 2 agents she seemingly held with deep admiration. "I don't understand though. Why would the foreman go to so much trouble, and why magnetite?"

Morales shrugged. "We may never know, the FBI searched his place and found nothing. So unless he was part of a terrorist organisation, and they strike again, we will never know." She sighed. "Anyway, your dismissed." Reyes and Doggett left the room and as they went to the parking lot, Reyes told Doggett what Marita had told him.

Doggett obviously had a hard time believing what he had just been told. "You believed everything she said?"

Reyes shrugged. "She had no reason to lie, and I think this means there's a new conspiracy around for us to expose." She said eagerly. 

"Alright, I can believe that." Doggett mentioned as he and Reyes said goodbye for the night.

**Notes for the Chapter:**

> Author's note: If your familiar with the beginning, that's because it's from the season 10 comics. There's going to be material from all kinds of different mediums in this story.


	5. End of The Beginning: epilogue

**Summary for the Chapter:**

> New stuff is established.

Later that night...

Reyes got home and something felt off. Suddenly, she saw a figure sitting in the shadows, Reyes pointed her gun at it.

"Freeze!" She demanded, but the figure didn't respond. Reyes turned the lights on and gasped. There was a man dressed in a black ops uniform, with a bullet hole in his head. Blood was everywhere and there was a gun on the floor, and no bullets had been fired from it.

"I apologize for the rude meeting, but I had to save you." A voice said. Reyes spun around and saw an African woman. She was dressed in a trench coat and had red hair. Anyone who was an Annie Lennox fan would mistake for a transvestite.

"Who are you?" Reyes demanded, her gun aimed at the figure.

"Are you familiar with MR.X?" the figure asked.

Reyes thought for a bit. "Mulder's second informant?"

"Correct." The figure said. "You may call me MRS.X"

"Your going to be my informant?" Asked Reyes, lowering the weapon.

"For the NeoSyndicate." MRS.X confirmed.

"So Marita was telling the truth." Reyes mused.

"Don't tell Doggett, the less people know about me helping you, the better."

"Makes sense." Reyes agreed.

"Now if you excuse me, I'm almost late for a meeting. You dispose of the body." MRS.X said and left. Reyes just threw her arms up in frustration and gathered any flammable materials to burn the body.

\-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Later that evening...

The NeoSyndicate were meeting.

"This is a disaster. We failed to in our objective to get rid of Gibson Praise." The red-haired woman said angrily.

"It could be worse." The fat man replied.

"I agree, at least Reyes and Doggett has no idea we're involved." MRS.X said.

The brown-skinned man sighed. "It's a shame we couldn't kill them now and get rid of our troubles. But sadly, they joined Mulder's religion and if they were killed now, it would be turned into a crusade."

"What does that even mean?" The red-haired woman said in annoyance.

"It means that Doggett, Reyes, The Lone Gunmen and the UFO nuts will go mad, team-up and take us down." The brown-skinned man explained. "At least while their alive, we can stop them. All we have to do, is make sure we can keep this up for another 11 years."

The end of the Beginning of the End.


	6. Secrets prologue

**Summary for the Chapter:**

> A bad vision

A man was running through a large storage area, there were tall shelves and boxes everywhere and the man was wearing a suit. He was wearing a suit and was moving very frantically. Eventually he stopped and started looking through boxes and files. Eventually he found what he was looking for; a small file. Inside the file, was a microchip. The man took it out and swallowed it. He continued doing this for all the other files, including a bee.

He made a mess of everything before running to a door and went through it. The door led a stairway, which let to a corridor in the Pentagon. The man ran down the corridor, and past an office where a woman sitting in a desk looks at him worried.

"Mr. Marx?" Asked the woman at the desk.

The man ignored her as he ran into his office and locked the door. He looked into the mirror and saw how sweaty and sick he looked.

He turned to the window and saw how beautiful it looked outside, with trees moving in the breeze and gentle fluffy clouds occupying the skies. He felt very distressed, with teary eyes and little sad smile. He closed his eyes and saw a quick flash of everything on fire and explosions everywhere. He also saw people being stung with bees and collapsing everywhere, with UFO's hovering in the orange sky.

'So that's what is going to happen if colonization goes ahead' he thought as he opened his eyes and heard the woman knocking at the door. Ignoring her, he took a picture frame from the bookshelf and broke it on the corner of his desk, causing spilling glass shards everywhere.

The woman sounded desperate. "Mr Marx, please open the door!"

Continuing to ignore her, the man picked up a glass shard before cutting his wrist and used the blood to write on the wall. After doing so he got out a pack of Morley's cigarettes and stuffed his mouth full of them.

Meanwhile, the military police had shown up. "Mr. Marx sir, if you don't open this door we will be forced to take physical action."

The man lit up all the cigarettes before getting out a gun and shot himself in the head.

The woman screamed as the military police broke down the door. The man's dead body lay dead on the floor, with a binary code sequence written on the wall: 01000100 01001001 01000111 00100000 01010111 01001001 01001100 01001100 01001001 01000001 01001101.


	7. Secrets chapter 1

**Summary for the Chapter:**

> An old friend....

Later that day...

Doggett arrived at the X-Files office, late.

"Good morning Monica." Doggett said, somewhat nervously.

"It's the afternoon." Reyes deadpanned, while reading an X-File.

Doggett shrugged. "My alarm clock was out of battery's and I had to buy new ones."

Reyes rolled her eyes. "Whatever, did you hear about the Pentagon Suicide?"

"Yes ,it's buzzing all over the place! A Robert Marx, He was a Secretary of Defense. What about it?" Doggett replied.

"We've been assigned to it."

Doggett was confused. "Why? That sounds like something regular security could handle."

"You would be right. However, before committing suicide, Robert wrote something on the wall. More accurately, it is related with one of the first X-File's Mulder and Scully ever investigated." Reyes said, and handed Doggett the file she was reading.

Doggett started reading the file. "A young boy named Kevin Morris was receiving messages similar to what Robert wrote down shortly after his sister was abducted. Mulder and Scully showed up, found the sister, but the mother refused to cooperate further and the case was closed."

Reyes nodded. "Both messages are binary codes. All data can be translated into computer binary code."

Doggett continued reading. "The Kevin messages were random. An image of art by DaVinci, musical notes, some religious text. What connection do these cases have? Besides the fact they both involve codes."

"Well the lab technicians have translated the Robert codes." Reyes said. "And it reads: Conrad Strughold is in the NeoSyndicate, and Kevin Morris can find him."

Doggett frowned. "Who else knows about this?"

" Well Leyla Harrison was able to limit the number of people who knew about this to just the lab technicians who translated it, herself, A.D Morales and Skinner." Reyes explained.

"Smart woman. No wonder she stopped being a field agent" Doggett remarked. Reyes felt jealous for some reason, but stayed silent. "Anyway, what about the autopsy?"

"I was about to perform it." Reyes said, standing up. "Come on." She said as she left the office, and Doggett followed her.

"Why didn't your perform it earlier?" Doggett asked as they waited for the lift.

"Because of the victim's identity and location of employment, it makes it critical that the media does not find out about this." Reyes replied as they got into the lift.

Doggett was able to guess what Monica was talking about. "So I have to make sure nobody tires to take any pictures or anything of the autopsy to leak it to the media.

"Correct." Reyes relied as they got out of the lift, walked down a corridor's and ended up in the autopsy room, where Harrison was waiting for them.

After making the necessary introductions, Reyes started the autopsy while Harrison and Doggett talked about the case.

"What's strange is that nobody knows why he wrote the message in blood when he had pen and paper in his office! This is definitely an X-File!" Harrison proclaimed.

Doggett read Marx's medial profile. "It says here that he was a non-smoker, so why did he stuff a pack of Morleys into his mouth before killing himself."

"Maybe he was trying to tell whoever was working on the X-Files that Mulder and Scully's arch nemesis; C.G.B Spender, is alive and up to no good!" Harrison suggested.

Doggett ignored her. "And the receipt in his pocket says that he brought the pack this morning, so he must have planned this in advance. But why go into all the trouble? Why didn't he just kill himself at home?"

"I spoke to the owner of the shop where he brought the pack, he said that Mr Marx looked fine and healthy." Harrison commented.

It was that moment that Reyes came out of the autopsy room. "Robert died of a self-inflicted gunshot to the head." She stated. " I also found a microchip and a bee in his stomach."

Doggett was in disbelief. "A microchip and a bee?"

"The microchips were used by the conspiracy to monitor and kill abductees." Harrison explained. "And the bees were also used to carry smallpox and the black oil."

"The black oil?" Doggett said, almost getting PTSD flashbacks of what happened last time he encounter them.

"Well it's obvious what we have to do." Reyes announced. "We need to find Kevin Morris, now."


	8. Secrets chapter 2

**Summary for the Chapter:**

> Doggett and Reyes interview a grown-up person.

The next day... In Sioux City, Iowa.

Doggett and Reyes pulled up outside of the address of the Morris's. They got out of the car before walking to the front door and knocking on it. A teenager opens it.

"Can I help you?" He asked.

Doggett and Reyes presented their FBI badges.

"I presume that your Kevin Morris?" Doggett asked.

"So what if I am?" said the teenager.

"Well if you are, something that might be related to you just happened in the Pentagon." Doggett explained.

The teenager was surprised by this. "Come in." Said Kevin. Doggett explained everything about Mr Marx, how it was related to Kevin, and what happened to Mulder and Scully.

"At least they got a happy ending." Kevin sighed. "Too bad my family won't get one."

"Is it happening again?" Reyes asked.

"Yes, but it's much worse this time." Kevin replied. "Before I remember the TV, the signal was just whispers from the TV." Kevin's eyes widened. "Now... oh... But NOW they are attacks! Horrendous attacks, Mr. Mulder I swear my brain was melting and it's so painful, there is a loud hum..."

"A hum?" Reyes asked.

"Like if someone had a speaker turned up too loud or some wires were crossed. As if the signal was coming from a machine, its metallic." Kevin explained.

Doggett was looking at some papers he and Monica had picked up on the way. "We saw you went to the hospital recently. You had an attack at a park bench, the people that helped you said blood was coming from your nose."

Kevin shrugged. "Yes, they uh... well I didn't tell the doctors about all of THIS. They said it could have been anything maybe low blood pressure or something. They did a scan on me and found nothing. Everything was clear."

"You didn't tell the doctors about your mother?" Doggett asked.

Kevin was confused. "Why would I?"

"Well she died from a brain tumor Kevin, her symptoms described where very similar to yours." Doggett explained.

"Wait.. what you DON'T BELIEVE ME!?" Kevin screamed.

"Look, I want... I just want answers. We will help you get to the bottom of this." Doggett assured Kevin, who calmed down. Doggett continued. "What about your sister?"

"My sister disappeared." Kevin said.

"I know." Doggett replied. "we couldn't find anything on her. Any ideas where she could be? Maybe if we can get her checked out it could provide some medical history and after we get you to the doctor and tell them we could..."

Kevin interrupted him. "My sister was taken. She was abducted again and never returned."

Doggett went silent.

"And now. I'm supposed to find this Conrad Strughold, how?" Kevin ranted.

Suddenly, Kevin begins to convulse violently and falls to the floor.

Reyes quickly held down Kevin while Doggett called the ambulance.

As the ambulance arrived and took Kevin to the hospital, with Doggett and Reyes following it in their car, nobody noticed the white van with the Strughold Mining Company logo on it, following them.


	9. Secrets chapter 3

**Summary for the Chapter:**

> More questions

Later that day, at the hospital...

The Doctor who had just examined Kevin, gave Doggett and Reyes the bad news.

"We've done a scan on him and he has a brain tumor."

Reyes was confused. "What?"

The doctor was embarrassed. "We don't know how to explain it either, because it wasn't there last time he came in."

"How can he have a brain tumor over night?" Doggett asked.

"I don't know, nobody knows. And I saw this thing on the scan. Its massive, and he may not wake up from this." The Doctor replied.

"Is it possible someone did this to him?" Reyes asked.

"You're are talking about cancer gene manipulation?" The doctor said in disbelief before walking back into the room where Kevin is.

"Monica, what is going on?" Doggett asked.

"Isn't it peculiar? His mother? An ex abductee, died from brain cancer. His sister? Who knows? And now him? There is no history of brain cancer in their family." Monica mused. "Maybe the NeoSyndicate are up to something?"

"If that is the case, then why are they doing this?" Doggett asked.

Suddenly, the doctor came running out Kevin's room. "He's awake."

Doggett and Reyes ran into the room, where Kevin looked like he was on his deathbed.

"I know what the codes are now." Kevin panted out. "It's coordinates to where Conrad Strughold is."

Kevin grabbed Doggett's head and whispered the coordinates into his head. Before falling back down onto the bed and dying. Doggett and Reyes exited the room and Doggett called the Lone Gunmen and gave them the coordinates.

"That's in Tunisia." Langley said.

"There's no images of it on google maps." Byers chimed in.

"Whoever this is, their well connected." Forhike stated the obvious.

"Can you get us there discreetly?" Doggett asked.

"Yep." Langley replied.

"Do it." Doggett commanded, and hung up before turning to Monica. "We're going to Tunisia."

**Notes for the Chapter:**

> Author's note: This story part of the story is adapted from the fan-written script: The X-Files: Syndicate Control, by Jack Venturo. While I liked it, I had these problems with it:
> 
> 1: Mulder would NEVER just leave Scully without talking to her about it first (and I refuse to read any MSR break-up fic).
> 
> 2: The subplot with Miller and Simmons just distracted and slowed down the plot.


	10. secrets chapter 4

**Summary for the Chapter:**

> Doggett and Reyes arrive in Tunisia.

48 hours later...

Doggett and Reyes stopped their car outside a tall desert dune. They got out and walked up the hill before Doggett pulled out a pair of binoculars, while Reyes pulled out a telescope and they stared at what they saw: miles of cornfields and domes.

"This matches the description of the cornfields, domes and bees Mulder and Scully saw after the X-Files were burned." Reyes commented.

"But what are they doing here?" Doggett mused.

"If I remember the report that Mulder wrote about it, they were genetically modifying the corn and bees to carry the black oil to spread across the world when the aliens come to colonise the Earth and make them masters of the universe." Reyes explained.

Doggett snickered.

"Be a skeptic all you want, but the colonisation is not happening." Reyes replied. "And now, we have to find out what was so important Robert Marx killed himself to give us these coordinates." Reyes concluded.

Doggett nodded and they carefully made their way down the dune. Doggett thought about how they got here. They had gotten the Lone Gunmen to create fake passports and booked various flights to get them to Tunisia. After informing A.D Morales about chasing a lead about the murder, they got to the airport and the next 48 hours were spent sleeping and changing flights until they arrived in Tunisia. They went to a clothes shop, changed out of their suits and into what they were wearing now. Reyes was wearing a white blouse, green jeans and black boots. Doggett was wearing a blue t-shirt, blue jeans and black trainers. They then got a rental car and drove to the coordinates.

Reaching the bottom of the dune, Doggett and Reyes hid in the cornfield.

"What now?" Doggett asked.

"Now, we confirm that they are still doing genetic modification on corn and bees. Afterwards, we find Conrad Strughold and get some answers." Reyes explained.

Doggett nodded and they opened the door to one of the domes, and they saw bees flying around. They quickly shut the door.

"Ok, it seems like their still doing the genetic modifications, how do we find Conrad Strughold?" Doggett asked.

Reyes began to think for a moment, when something unexpected happened.

"Look!" She shouted, pointing to the sky. UFO's appeared and men dressed in robes.

"Those must be from the same military program that created the super soldiers!" Doggett cried out.

Reyes couldn't be bothered to argue with Doggett's skepticism, and instead looked at what was coming out of the UFO's lights that were beaming down.

"They look like what the foreman was wearing when he attacked me at the oil pipeline." Doggett pointed out.

"These could be the Acolytes Marita told me about, but if they are, then what are they doing here?" Reyes mused.

Suddenly, there was a combination of flames, explosions and screaming.

"Their destroying this place!" Reyes realised. "But why?"

"You can wonder why later!" Doggett cried out. "If we don't get out of here soon, we're dead!"

Realising he was right, Reyes grabbed Doggett's hand and they ran until they reached the road, where multiple trucks were riding across it.

"Come on!" Reyes called out, and she and Doggett climbed into the back of one of the trucks.

"What now?" Doggett asked.

"Now, we wait and see where we go." Reyes answered.

From there they waited until they reached the airport, where they saw a massive cargo plane. Various trucks were being loaded onto the plane, including the one they were on.

"Wait until we're airborne, then we go track down Strughold." Doggett said.

Reyes nodded and the 2 of them made sure they stayed hidden for a while.


	11. Secrets chapter 5

**Summary for the Chapter:**

> The confrontation you've been waiting for.

An hour later...

Doggett peaked his head out of the truck he and Reyes were hiding in.

"The coast is clear." He said softly and the 2 of them got out of the truck.

"Ok, here's the plan." Reyes explained, having thought of what to do.

After a few minutes of explaining, Doggett looked confused. "Are you sure that's a good idea?"

"Yes." Reyes insisted. "We need an insurance policy to escape in case we get caught or they try to kill us."

Doggett sighed. "All right."

Reyes smiled. "Good, now go off and do that. I'm going to do what I need to do."

Doggett nodded and snuck off. The thing Reyes needed to do, was to find Conrad Strughold. She needed to know how the Syndicate were formed, and what his role in it was. She had no idea how to find him, so she just sneaked around for a bit before she found the kitchens, where she heard from chef's being self-congratulatory.

"I love how Mr Strughold only has herbal essences, it's healthy for him." One of them said.

"Well maybe that's how he's lived for so long." The other said.

"How old is he anyway?" The first one responded.

"Nobody but him knows, but my best guess would be somewhere between 70-100 years old." The other responded.

"Right, well if you excuse me, I need to deliver these to him, if I wait too long I might get killed!" The first one said, saying quickened farewells before he exited the kitchens.

Reyes hid and followed him until he reached Strughold's office. The chef entered a code on the wall next to the door and entered the office. Reyes slowly snuck up behind him and thanks to growing up in Mexico, where she had to learn various stealth moves in order to survive, and quickly hid behind a piece of furniture.

Reyes looked under the sofa and saw only 2 pairs of feet in the room, one of them behind a table. She heard what they were saying:

"What do you think sir?" The chef asked.

She heard Strughold sipping the tea. "That's very good thank you. You may leave the room now, and make sure I am not disturbed for half an hour."

The chef nodded and left the room. Reyes then heard a gun being cocked and Strughold saying. "You, behind the sofa, come out with your hands above your head!"

Reyes had no choice but to comply as she stood up slowly.

"So you're Conrad Strughold." Reyes stated. "I've been wanting to meet you ever since Robert Marx committed suicide and left a clue that helped me find you."

"And that clue led to Kevin Morris, whom we weren't able to kill quick enough to prevent him from telling you were I was." Strughold stated.

"Mulder's notes never mentioned you." Reyes stated.

"Because I was careful enough to not reveal my existence to him, unlike that fool Spender and the rest of the conspiracy." Strughold hissed. "I was born in Germany in the 1920's, and my father was Hubertus Strughold, who experimented on Jews during World War II and was sent to the United States of America as part of Operation Paperclip."

Reyes thought for a bit. "Isn't that an operation by the US Military to retrieve Nazi scientists after World War II?"

Strughold nodded. "After the war, Nazi scientists were secretly brought to the U.S. for work on a variety of projects, including the space project and the attempts to create an alien-human hybrid."

Reyes started to piece together what happened. "And that's where you met C.G.B. Spender, Bill Mulder and all the other conspiracy members."

Strughold nodded again. "We formed it as a secret group and we started in 1952. This lasted until 1973, where officially broke off ties with the United States government and formed our alliance with the aliens."

"I already know about the alliance and your efforts to create a human/alien hybrid." Reyes interrupted. "But I want to know it why you were never present."

Strughold exacerbated. "Because it required everyone to give up a loved one. I did not have any loved ones, we all agreed that I should be the leader of the conspiracy, which we called the Syndicate for simplicity's sake, and that my existence would be kept secret."

"You didn't love your father!?" Reyes almost cried out.

"He was too busy with NASA to care what I was up to." Strughold explained. "He barely bat an eyelid when I retreated to Tunisia to continue the project."

"And you only left for important meetings." Reyes stated.

"Correct. It's why I wasn't present when the rest of the Syndicate were burned to death by the rebels." Syndicate explained. "And then Spender tried to resurrect the project, and was killed for it."

"You don't sound very upset." Reyes stated.

"Why would I? The less idiots like Spender I have with me, the better." Strughold sneered. "So I went back to some of the older members of the Syndicate, who left over differing opinions, and we formed the NeoSyndicate."

"And now your trying to convince the aliens to colonize the Earth." Reyes stated.

"Clever girl, care to explain how you know?" Strughold asked.

"Answer this first, why? Why try to convince the aliens to colonize the Earth after they changed their mind after multiple failures? The only reason why the Syndicate was formed in the first place, was to ensure that some of humanity would survive."

Strughold smiled. "Humanity has too much freedom and is heading on a path of self-destruction. By being made slaves to the aliens, we course-correct them before forcing the aliens to retreat."

Reyes was confused. "How?"

Strughold grinned. "You don't get to know, as your going to die now?"

Reyes was even more confused. "Then why did you tell me your entire backstory and plan, if you were just going to kill me?"

"Because you'll die with the knowledge that you made more progress in less than a year, than Mulder did over 10 years!" Strughold stated, preparing to pull the trigger.

Suddenly, the door opened, and a dead guard fell on the floor. Before Strughold could react, he was shot in the head. This caused blood to splash everywhere and Strughold slumped down on the table, dead.

Reyes spun around and saw Doggett. "John!" She cried out and hugged him. "Did you do what I asked you to do?"

"Yes." Doggett answered.

Suddenly, they heard the sound of armed guards approaching. "Then let's get out of here!" Doggett said.

Reyes nodded and they ran down to the cargo hold, where Doggett opened the cargo door before getting in a helicopter and flew out of the plane. Reyes got the remote detonator and pressed it, blowing up the plane.


	12. Secrets epilogue

The next day...

Morales was reading the report with great interest. "I see, and what happened after you got off the plane and blew it up?"

"Since we were over Europe, we flew to England and got a plane from there back to Washington." Doggett explained.

"I see." Morales replied. "Well since you've taken out someone who is undoubtedly one of the NeoSyndicate highest ranking members, I don't think they'll be doing anything major for a while."

"So what are we supposed to do in the meantime?" Reyes asked.

"Go investigate some stand-alone cases." Morales answered back. "I'm trying to get the FBI to take the X-Files more seriously, and closing some of the open X-Files that were never closed will help do that."

Doggett and Reyes nodded before leaving the room.

"It would also be nice if you could find incontrovertible, scientific proof of the existence of extraterrestrials that cannot be brushed away. I wish Mulder and Scully would have done that, but they were too busy having sex to do so." Morales sighed.

\---

Meanwhile, the members of the NeoSyndicate were not happy.

"So, Doggett and Reyes are a bigger threat then we thought." The white-haired man said.

"I think we should not make any major moves for a while, keep them of our backs." The red-haired woman replied.

"I concur." The brown-skinned woman finished.


	13. Jump the Shark: Alternate Ending

**Summary for the Chapter:**

> How 'Jump the Shark' should have ended.

Frohike looked at Langley and Byers. "Guys?"

He motioned to the door with his eyes, Langley and Byers nodded. "Whatever it takes".

Frohike looked back at the professor, who was staring at them. Frohike reached for the fire alarm switch as Langley and Byers slowly moved backwards, before pulling the switch and the 3 of them ran below the door as it shut. The professor released what was happening and raced for the door, but it was too late, as the door shut in his face. Jimmy and Yves raced round the corner and joined the gunmen in watching the professor convulse on the floor. A strange, pink liquid stained his shirt, and a pool of the liquid is collected around his mouth on the floor.

"Well that was a close one." Langley commented.

"Your telling me, I thought I wasn't going to make it." Frohike commented.

"It could have been worse, we could stood there like complete morons for no good reason while the door closed and died for no good reason." Byers shot back.

The Gunmen smirked, safe in the knowledge that they could retire and their paper could live on via the next generation of conspiracy theorists, government watchdogs and computer hackers.

24 Hours later...

"So what are you going to do now that your retired?" Asked Jimmy, as the Lone Gunmen loaded up their 1974–79 VW Transporter.

"Well Mulder has told us that the man responsible for investigating the first ever X-Files, Arthur Dales, lives in Miami and said that we can live with him for a while." Byers said.

Jimmy nodded. "I'm going to miss you guys."

Langley smiled. "If Arthur has any interesting stories about his time on the X-Files, then we'll send them to you to publish."

"That sounds like a good plan." Yves replied.

"Afterwards, we'll probably tour America, seeing sights we've always wanted to see and enjoying life for a change, as long as we avoid Miami." Forhike said.

Everyone laughed at that, before they said their goodbyes and Byers, Frohike and Langley drove off to Goodland, Florida.

"So what do we do now?" Jimmy asked.

"Upgrade their primitive tech and start publishing the paper." Kimmy the Geek said, entering the loft apartment.

"Sounds like a plan." Yves said as she went back into the apartment, followed by Jimmy, to begin the paper anew.


	14. Ghosts of the Machines: Prologue

**Summary for the Chapter:**

> An unexpected sequel

Claude Peterson was happy for the first time in 8-9 years. He worked for the department of Defense and his first assignment was to gain access to the Central Operating System or (C.O.S.), an advanced AI that a Well-Fed Man ordered him to acquire. Claude then spent 2 years trying to acquire it with no success. Suddenly, it started killing people and he almost got his hands on it, but then 2 FBI agents prevented him from doing so and uploaded a virus that destroyed it. As punishment, he was put behind a desk and he slowly began to feel miserable.

His brother on the other hand (Who had got married and changed his last name to Pennock) had not only met and worked with the FBI agent's who ruined Claude's carrier, he had gotten a promotion from detective to police chief. Claude hadn't spoken to him since.

Finally, after years of being miserable, Claude got his big break. The Well-Fed Man was killed, and because of how high-ranking he was, the DOD was in chaos. Claude took this opportunity to start moving up.

After he discovered about the alien colonisation of the Earth, and them cancelling it after deciding to stop their in-fighting and colonise other planets instead. He also discovered that various pieces of evidence from the X-Files where kept in the basement, he decided to go down there and see if the C.O.S. was down there. And it was.

"If I had known you were down here all this time, I would have come down earlier." Claude said, pushing the on button, nothing happened. "Your creator died of a heart attack before he could tell us how to restore you. However, I am going to put some engineers on restoring you and getting my revenge on the F.B.I. While the specific agents in question have retired and not worth tracking down, we can now inconvenience the current X-Files agents." Claude stated as he went off to arrange restoration of the C.O.S., unaware that it didn't need restoration.

Entering the lift, Claude pressed the button to the top floor and just before it reached there, the lift then broke at it's hinges and plunged to the ground. Claude realised what was happening. "It's alive. But how!?" Claude screamed out as he plunged to his death.


	15. Ghosts of the Machines: chapter 1

**Summary for the Chapter:**

> Skinner talks to Doggett and Reyes about the seriousness of the situation

Doggett was sleeping when his phone rang. He shot out of the bed and picked it up. "Hello?"

"Doggett, it's Skinner. Meet me and Reyes at Capitol Hill in 1 hour." The call ended.

Doggett just sighed before getting up, getting dressed and driving to Capitol hill, where he met up with Skinner and Reyes.

"I just got word that the Depart of Defense is under attack." Skinner explained.

Doggett felt shocked. "By who?"

Skinner just stared at Doggett and Reyes. "By an X-File."

Reyes was shocked. "What?"

"Some computer system known as the Central Operating System or (C.O.S.), came to life after being dormant for almost a decade and is currently murdering employees all over the building." Skinner explained.

Reyes searched her memory. "Mulder and Scully investigated the COS back in their early days. It was personal for Mulder as that's how one of his old partners was killed." She stared at Skinner. "And they weren't under your supervision at the time."

Skinner nodded. "Since the conspiracy didn't see them as a big threat at the time, their main tactic was just changing who their supervisor was. Since the X-Files was closed when I was their supervisor, I ended up being their supervisor for the rest of their time on the X-Files".

Doggett decided to get to the point. "And you had to tell us this out of the office because?"

"The DOD, that's where Mulder got the cure for Scully's cancer. It's where all of the evidence of the X-Files is kept." Reyes realised.

"And if that evidence was ever released to the general public..." Skinner started.

"Then there would be a mass panic and possibly start a revolution against the government." Doggett finished.

"And if the C.O.S. figures out how to use the internet.." Reyes couldn't bring herself to finish the sentence.

"That's why you two have to get in the DOD and stop it." Skinner explained. "Morales is currently arranging for the two of you to sneak into the DOD and shut down the C.O.S."

"I'll go visit the New Lone Gunmen and see if they can figure out how to shut it down." Reyes explained.

"Meet me in my office at 17:00." Skinner ordered. Doggett and Reyes nodded.


	16. Ghosts of the Machines: chapter 2

**Summary for the Chapter:**

> Reyes finds out how to destroy the machine

Reyes went to the lair of the New Lone Gunmen, and explained everything that was happening to Kimmy the Geek and gave him the original case files.

"Of course the C.O.S. is still alive." Kimmy exclaimed. "This Brad idiot only made the virus to wipe-out the current version of the C.O.S, not the back-ups!" He sounded annoyed as he started to type on his computer.

"So, how do we get rid of the C.O.S. and it's back-up?" Reyes asked.

Kimmy finished pressing a few buttons and a CD was extracted from it. "Put this CD into the C.O.S. CD drive and it will wipe it out." Kimmy explained, Reyes looked amazed. "I have a virus for every occasion." He continued.

"OK?" Reyes said, taking the CD. "Thanks." She said, leaving the lair.


	17. Ghosts of the Machine: Chapter 3

**Summary for the Chapter:**

> Doggett and Reyes infiltrate the DOD.

Reyes and Doggett met with Skinner in his office, where Reyes explained how to defeat the C.O.S.

"I see." Skinner explained. "A.D. Morales is currently arranging for you to sneak in undercover as members of a S.W.A.T team. Officially they are there to rescue anyone still alive in the building. Unofficially, there are there to destroy all evidence of the C.O.S, including any evidence of the X-Files."

Reyes just sighed. "If Mulder and Scully were her right now, then they would release the files without hesitation. I feel like we're failing them."

Doggett comforted her. "You were rather have mass riots?"

Reyes sighed. "No, your right."

Suddenly, Skinner answered his phone and hung up. "That was Morales, it's time."

Doggett and Reyes quickly got changed into S.W.A.T team uniforms before jumping on the helicopter with the rest of the team. Everything was going smoothly, until just before reaching the DOD rooftop. Drones charged towards the helicopter.

"Everybody out!" The S.W.A.T leader ordered.

Since there were just a few feet above the roof, everyone just landed roughly on their backs while the helicopter flew off. Suddenly, the drones charged at the S.W.A.T members. Doggett grabbed Reyes and they ran inside an entrance while the rest of the team shot at the drones.

\---

"That was close." Doggett commented, as he and Reyes got inside and shut the door behind him.

"Don't speak to soon." Reyes pointed down.

Doggett did the same and saw multiple robots marching around the DOD.

"What are they?" Doggett asked.

"The C.O.S. probably constructed them using classified documents and spare parts." Reyes theoriesed.

"Well we're about to find out if they're susceptible to firearms." Doggett shouted.

Reyes turned and saw a robot approach them. It looked like a miniature version of the ATST from Star Wars. Doggett cocked his shotgun and fired, causing the robot to explode.

"Well that was easy." Doggett commented.

"I wouldn't speak too soon." Reyes pointed at something.

Doggett turned around and saw an army of identical tiny robots charge towards them.

"Run!" Doggett screamed out and fired the shotgun at the robots before running behind Reyes. Reyes would occasionally stop briefly and fire her sub-machine gun at the robots that were getting too close to Doggett before running again.

Eventually, Doggett and Reyes came across the C.O.S. Reyes shot at it multiple times to prevent it from activating any close-range defenses. She then went up to it and inserted the CD into it's disk-drive, while Doggett shot anymore incoming robots.

"Destroy me, and you'll destroy the X-Files evidence." The C.O.S begged.

"And let you kill more innocent people? No thanks." Reyes replied, hitting the enter key.

"NO!" The C.O.S screamed as it blew up. Doggett and Reyes quickly ran back to the roof as the C.O.S, along with all evidence surrounding the X-Files, were destroyed.


	18. Ghosts of the Machine: epilogue

**Summary for the Chapter:**

> The aftermath

"So, all the evidence is gone?" Kimmy the Geek asked.

Reyes nodded. "All the evidence from the X-Files Is now gone. Every file not in the basement office, various implants and who knows what else, gone forever."

"And my disk?"

Reyes pulled out a CD case with a burnt CD inside. Kimmy took it. "Well, at least I might be able to retrieve the virus off this."

"Why not just purchase a version of the virus?" Reyes asked.

"Because then people might start tracking me, and I would like to stay under the radar, thank you very much!" Kimmy responded passionately.

Reyes nodded. "Well I have to be getting back to work, good luck."

Reyes left, just as Jimmy and Yves were coming out of the bedroom.

"She is so annoying." Yves commented.

"Not as annoying as your loud sex was before I inserted sound-proof walls." Kimmy commented. "Anyway, I hope I can fix the CD."

Jimmy felt suspicious. "Why?"

Kimmy smiled. "Wait and see my friends, wait and see."

\---

There were 3 people in the dimly-lit room. A fat white-haired man at the the side, a red-haired woman sat on the other side and a brown-skinned woman sat the other end. The empty presence of Strughold at the head of the table could be felt.

"Well the C.O.S. got destroyed." The red-haired woman sighed. "Oh well, at least the X-Files evidence is gone."

"Indeed." The white-haired man smiled. "I think it was retribution for Sturghold's death."

"Anyway." The brown-skinned woman. "We should get back to trying to convincing the aliens to colonise the Earth."

The other 2 nodded and they started to start discussing their next plan of action.


	19. Dreams

**Summary for the Chapter:**

> The Dream Lord visits Monica

Monica Reyes woke up in a cold sweat. She quickly reached over for the phone and paused. She couldn't call Doggett, she didn't need his idiotic skepticism right now, she needed someone more open-minded. She picked up the phone and dialed a number.

The phone rung and the voice on the other end picked up. "Hello?"

"Hey Marita, I need to talk to you." Monica said.

Marita yawned. "Why?"

"Because I've just had some bad dreams, and they felt real." Monica replied.

"Go on." Marita responded.

Monica then talked about her dreams for a few hours. About how it opened with Mulder running away, Kersh being allowed to remain Assistant director for lack of evidence and the super soldiers were everywhere. It got more stupid and worse from there. Scully gave up William for some reason, the 2012 invasion was given completely contradictory information as to why it didn't happen, CSM claimed that he was William's father and everybody believed him despite lack of evidence, everybody acted completely random and nonsensically, and it ended with her being shot in the head.

"I see the Dream Lord has visited you." Marita said once Monica had finished.

Monica was confused. "Dream Lord?"

"It likes to mess with your mind at times of people with emotional vulnerability." Marita explained. "Back when the Syndicate was experimenting on me, and before CGB Spender cured me after they were destroyed, the Dream Lord visited me and taunted me with visions form an alternate timeline. It showed me what if me and Alex had met under different circumstances. It showed me how we could have been normal and had a family together, we just looked so happy."

Monica considered asking Marita how she and Krycek had met, but she decided that was a bit personal. "But I'm not emotional vulnerable."

"That's what you think. But in reality, you are." Marita replied. "I don't know how you are, only you can find that out."

Reyes thanked her and went back to sleep. No more dreams came that night, and she felt very confused.

**Author's Note:**

> Sorry for the short prologue, but it felt necessary to include. I promise the story will get better from here


End file.
